Sindbis virus is a membrane-containing virus with two shells of viral protein. Sindbis virus is a prototype of the genus Alphaviridae. The virus is composed of 240 copies each of three different structural proteins. Two of the proteins, E1 and E2 are glycosylated and are embedded in the virus membrane. The third is the capsid protein that forms a protein shell beneath the virus envelope. The capsid protein interacts with the 49S single stranded RNA genome and the C-terminal end of E2 spike protein to form the internal nucleocapsid structure. We have determined the three dimensional structure of Sindbis virus using electron cryomicroscopy and computer-aided image processing techniques. We have also recently determined the structure of a mutant of Sindbis called TRSBNE2G216. This mutant incorporates an unprocessed form of the E2 glycoprotein called PE2. The normally cleaved and discarded portion of PE2 is the E3 peptide. Although not incorporated into the structure of Sindbis virus, the related Semliki Forest virus is believed to include E3 in its outer shell. In this study, we use the difference map between the wild-type virus and its mutant to allow us to compare their structural differences and speculate how these differences influence function.